Skip to main content
Open Access Publications from the University of California

Virmid: accurate detection of somatic mutations with sample impurity inference

  • Author(s): Kim, Sangwoo
  • Jeong, Kyowon
  • Bhutani, Kunal
  • Lee, Jeong
  • Patel, Anand
  • Scott, Eric
  • Nam, Hojung
  • Lee, Hayan
  • Gleeson, Joseph G
  • Bafna, Vineet
  • et al.

Abstract Detection of somatic variation using sequence from disease-control matched data sets is a critical first step. In many cases including cancer, however, it is hard to isolate pure disease tissue, and the impurity hinders accurate mutation analysis by disrupting overall allele frequencies. Here, we propose a new method, Virmid, that explicitly determines the level of impurity in the sample, and uses it for improved detection of somatic variation. Extensive tests on simulated and real sequencing data from breast cancer and hemimegalencephaly demonstrate the power of our model. A software implementation of our method is available at

Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.

Main Content
Current View